Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAGCGCAACAAAAGGAAAGCAGGGAAACCTCGCCGTCCTCTCTCTCCATCCATGCCCTAGCACGCGCCGCGCAGCCTACGAGCGGGAGCCACACCTCGAGgtaaccaccaccaccatcgccaccctcctcctcctcctcctcctcttctcccctcgatcccgtccgatcaaaaccctagcaccctccgcgcggcgctggc...

Basic information

species Oryza sativa
transcript LOC_Os03g49180.1
intron # 1
splice site 5'
intron type U2

Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|86902690|gb|CI306493.1|CI306493
EST:     CATGCCCTAGCACGCGCCGCGCAGCCTACGAGCGGGAGCCACACCTCGAG                         GTCTTCATCTGTTGCACTCATGATTTAGCACCAGCTGAAGTGACCTCTGAG
genomic: CATGCCCTAGCACGCGCCGCGCAGCCTACGAGCGGGAGCCACACCTCGAGgtaaccacca ... atttttacagGTCTTCATCTGTTGCACTCATGATTTAGCACCAGCTGAAGTGACCTCTGAG
EST: gi|88733678|gb|CI756855.1|CI756855
EST:     CATGCCCTAGCACGCGCCGCGCAGCCTACGAGCGGGAGCCACACCTCGAG                         GTCTTCATCTGTTGCACTCATGATTTAGCACCAGCTGAAGTGACCTCTGAG
genomic: CATGCCCTAGCACGCGCCGCGCAGCCTACGAGCGGGAGCCACACCTCGAGgtaaccacca ... atttttacagGTCTTCATCTGTTGCACTCATGATTTAGCACCAGCTGAAGTGACCTCTGAG
EST: gi|33684100|gb|CF312339.1|CF312339
EST:     CATGCCCTAGCACGCGCCGCGCAGCCTACGAGCGGGAGCCGCACCTCGAG                         GTCTTCATCTGTTGCACTCATGATTTAGCACCAGCTGAAGTGACCTCTGAG
genomic: CATGCCCTAGCACGCGCCGCGCAGCCTACGAGCGGGAGCCACACCTCGAGgtaaccacca ... atttttacagGTCTTCATCTGTTGCACTCATGATTTAGCACCAGCTGAAGTGACCTCTGAG
EST: gi|33663467|gb|CF294434.1|CF294434
EST:     CATGCCCTAGCACGCGCCGCGCAGCCTACGAGCGGGAGCCACACCTCGAG                         GTCTTCATCTGTTGCACTCATGATTTAGCACCAGCTGAAGTGACCTCTGAG
genomic: CATGCCCTAGCACGCGCCGCGCAGCCTACGAGCGGGAGCCACACCTCGAGgtaaccacca ... atttttacagGTCTTCATCTGTTGCACTCATGATTTAGCACCAGCTGAAGTGACCTCTGAG
EST: gi|88424612|gb|CI606411.1|CI606411
EST:     CATGCCCTAGCACGCGCCGCGCAGCCTACGAGCGGGAGCCACACCTCGAG                         GTCTTCATCTGTTGCACTCATGATTTAGCACCAGCTGAAGTGACCTCTGAG
genomic: CATGCCCTAGCACGCGCCGCGCAGCCTACGAGCGGGAGCCACACCTCGAGgtaaccacca ... atttttacagGTCTTCATCTGTTGCACTCATGATTTAGCACCAGCTGAAGTGACCTCTGAG
EST: gi|88742134|gb|CI765642.1|CI765642
EST:     CATGCCCTAGCACGCGCCGCGCAGCCTACGAGCGGGAGCCACACCTCGAG                         GTCTTCATCTGTTGCACTCATGATTTAGCACCAGCTGAAGTGACCTCTGAG
genomic: CATGCCCTAGCACGCGCCGCGCAGCCTACGAGCGGGAGCCACACCTCGAGgtaaccacca ... atttttacagGTCTTCATCTGTTGCACTCATGATTTAGCACCAGCTGAAGTGACCTCTGAG
EST: gi|426274|gb|D22135.1|D22135
EST:     CATGCCCTAGCACGCGCCG-GCAG-CTACGAGCGGGAGCCACACCTCGAG                         GTCTTCATCTGTTGCACTCATGATTTAGCACCAGCTGAAGTGACCTCTGAG
genomic: CATGCCCTAGCACGCGCCGCGCAGCCTACGAGCGGGAGCCACACCTCGAGgtaaccacca ... atttttacagGTCTTCATCTGTTGCACTCATGATTTAGCACCAGCTGAAGTGACCTCTGAG
EST: gi|38470481|gb|CF954612.1|CF954612
EST:     CATGCCCTAGCACGCGCCGCGCAGCCTACGAGCGGGAGCCACACCTCGAG                         GTCTTCATCTGTTGCACTCATGATTTAGCACCAGCTGAAGTGACCTCTGAG
genomic: CATGCCCTAGCACGCGCCGCGCAGCCTACGAGCGGGAGCCACACCTCGAGgtaaccacca ... atttttacagGTCTTCATCTGTTGCACTCATGATTTAGCACCAGCTGAAGTGACCTCTGAG
EST: gi|29662209|gb|CB658484.1|CB658484
EST:     CATGCCCTAGCACGCGCCGCGCAGCCTACGAGCGGGAGCCACACCTCGAG                         GTCTTCATCTGTTGCACTCATGATTTAGCACCAGCTGAAGTGACCTCTGAG
genomic: CATGCCCTAGCACGCGCCGCGCAGCCTACGAGCGGGAGCCACACCTCGAGgtaaccacca ... atttttacagGTCTTCATCTGTTGCACTCATGATTTAGCACCAGCTGAAGTGACCTCTGAG
EST: gi|4880874|gb|AU065173.1|AU065173
EST:     CATGCCCTAGCACGCGCCGCGCA-NCTACGAGCGGGAGCCACACCTCGAG                         GTCTTCATCTGTTGCACTCATGATTTAGCACCAGCTGAAGTGACCTCTGAG
genomic: CATGCCCTAGCACGCGCCGCGCAGCCTACGAGCGGGAGCCACACCTCGAGgtaaccacca ... atttttacagGTCTTCATCTGTTGCACTCATGATTTAGCACCAGCTGAAGTGACCTCTGAG
EST: gi|88583816|gb|CI701324.1|CI701324
EST:     CATGCCCTAGCACGCGCCGCGCAGCCTACGAGCGGGAGCCACACCTCGAG                         GTCTTCATCTGTTGCACTCATGATTTAGCACCAGCTGAAGTGACCTCTGAG
genomic: CATGCCCTAGCACGCGCCGCGCAGCCTACGAGCGGGAGCCACACCTCGAGgtaaccacca ... atttttacagGTCTTCATCTGTTGCACTCATGATTTAGCACCAGCTGAAGTGACCTCTGAG
EST: gi|88574754|gb|CI666523.1|CI666523
EST:     CATGCCCTAGCACGCGCCGCGCAGCCTACGAGCGGGAGCCACACCTCGAG                         GTCTTCATCTGTTGCACTCATGATTTAGCACCAGCTGAAGTGACCTCTGAG
genomic: CATGCCCTAGCACGCGCCGCGCAGCCTACGAGCGGGAGCCACACCTCGAGgtaaccacca ... atttttacagGTCTTCATCTGTTGCACTCATGATTTAGCACCAGCTGAAGTGACCTCTGAG
EST: gi|88826600|gb|CI777165.1|CI777165
EST:     CATGCCCTAGCACGCGCCGCGCAGCCTACGAGCGGGAGCCACACCTCGAG                         GTCTTCATCTGTTGCACTCATGATTTAGCACCAGCTGAAGTGACCTCTGAG
genomic: CATGCCCTAGCACGCGCCGCGCAGCCTACGAGCGGGAGCCACACCTCGAGgtaaccacca ... atttttacagGTCTTCATCTGTTGCACTCATGATTTAGCACCAGCTGAAGTGACCTCTGAG
EST: gi|88349341|gb|CI678322.1|CI678322
EST:     CATGCCCTAGCACGCGCCGCGCAGCCTACGAGCGGGAGCCACACCTCGAG                         GTCTTCATCTGTTGCACTCATGATTTAGCACCAGCTGAAGTGACCTCTGAG
genomic: CATGCCCTAGCACGCGCCGCGCAGCCTACGAGCGGGAGCCACACCTCGAGgtaaccacca ... atttttacagGTCTTCATCTGTTGCACTCATGATTTAGCACCAGCTGAAGTGACCTCTGAG
EST: gi|88344380|gb|CI677422.1|CI677422
EST:     CATGCCCTAGCACGCGCCGCGCAGCCTACGAGCGGGAGCCACACCTCGAG                         GTCTTCATCTGTTGCACTCATGATTTAGCACCAGCTGAAGTGACCTCTGAG
genomic: CATGCCCTAGCACGCGCCGCGCAGCCTACGAGCGGGAGCCACACCTCGAGgtaaccacca ... atttttacagGTCTTCATCTGTTGCACTCATGATTTAGCACCAGCTGAAGTGACCTCTGAG
EST: gi|88764771|gb|CI773889.1|CI773889
EST:     CATGCCCTAGCACGCGCCGCGCAGCCTACGAGCGGGAGCCACACCTCGAG                         GTCTTCATCTGTTGCACTCATGATTTAGCACCAGCTGAAGTGACCTCTGAG
genomic: CATGCCCTAGCACGCGCCGCGCAGCCTACGAGCGGGAGCCACACCTCGAGgtaaccacca ... atttttacagGTCTTCATCTGTTGCACTCATGATTTAGCACCAGCTGAAGTGACCTCTGAG
EST: gi|163923361|gb|EG711094.1|EG711094
EST:     CTACGAGCGGGAGCCACACCTCGAG                         GTCTTCATCTGTTGCACTCATGATTTAGCACCAGCTGAAGTGACCTCTGAG
genomic: CTACGAGCGGGAGCCACACCTCGAGgtaaccacca ... atttttacagGTCTTCATCTGTTGCACTCATGATTTAGCACCAGCTGAAGTGACCTCTGAG
EST: gi|88590171|gb|CI709004.1|CI709004
EST:     CATGCCCTAGCACGCGCCGCGCAGCCTACGAGCGGGAGCCACACCTCGAG                         GTCTTCATCTGTTGCACTCATGATTTAGCACCAGCTGAAGTGACCTCTGAG
genomic: CATGCCCTAGCACGCGCCGCGCAGCCTACGAGCGGGAGCCACACCTCGAGgtaaccacca ... atttttacagGTCTTCATCTGTTGCACTCATGATTTAGCACCAGCTGAAGTGACCTCTGAG
EST: gi|88574571|gb|CI666340.1|CI666340
EST:     CATGCCCTAGCACGCGCCGCGCAGCCTACGAGCGGGAGCCACACCTCGAG                         GTCTTCATCTGTTGCACTCATGATTTAGCACCAGCTGAAGTGACCTCTGAG
genomic: CATGCCCTAGCACGCGCCGCGCAGCCTACGAGCGGGAGCCACACCTCGAGgtaaccacca ... atttttacagGTCTTCATCTGTTGCACTCATGATTTAGCACCAGCTGAAGTGACCTCTGAG
EST: gi|88762619|gb|CI772175.1|CI772175
EST:     CATGCCCTAGCACGCGCCGCGCAGCCTACGAGCGGGAGCCACACCTCGAG                         GTCTTCATCTGTTGCACTCATGATTTAGCACCAGCTGAAGTGACCTCTGAG
genomic: CATGCCCTAGCACGCGCCGCGCAGCCTACGAGCGGGAGCCACACCTCGAGgtaaccacca ... atttttacagGTCTTCATCTGTTGCACTCATGATTTAGCACCAGCTGAAGTGACCTCTGAG
EST: gi|88578095|gb|CI674726.1|CI674726
EST:     CATGCCCTAGCACGCGCCGCGCAGCCTACGAGCGGGAGCCACACCTCGAG                         GTCTTCATCTGTTGCACTCATGATTTAGCACCAGCTGAAGTGACCTCTGAG
genomic: CATGCCCTAGCACGCGCCGCGCAGCCTACGAGCGGGAGCCACACCTCGAGgtaaccacca ... atttttacagGTCTTCATCTGTTGCACTCATGATTTAGCACCAGCTGAAGTGACCTCTGAG
EST: gi|88760868|gb|CI770424.1|CI770424
EST:     CATGCCCTAGCACGCGCCGCGCAGCCTACGAGCGGGAGCCACACCTCGAG                         GTCTTCATCTGTTGCACTCATGATTTAGCACCAGCTGAAGTGACCTCTGAG
genomic: CATGCCCTAGCACGCGCCGCGCAGCCTACGAGCGGGAGCCACACCTCGAGgtaaccacca ... atttttacagGTCTTCATCTGTTGCACTCATGATTTAGCACCAGCTGAAGTGACCTCTGAG
EST: gi|88826174|gb|CI776739.1|CI776739
EST:     CATGCCCTAGCACGCGCCGCGCAGCCTACGAGCGGGAGCCACACCTCGAG                         GTCTTCATCTGTTGCACTCATGATTTAGCACCAGCTGAAGTGACCTCTGAG
genomic: CATGCCCTAGCACGCGCCGCGCAGCCTACGAGCGGGAGCCACACCTCGAGgtaaccacca ... atttttacagGTCTTCATCTGTTGCACTCATGATTTAGCACCAGCTGAAGTGACCTCTGAG
EST: gi|33690596|gb|CF318835.1|CF318835
EST:     CATGCCCTAGCACGCGCCGCGCAGCCTACGAGCGGGAGCCACACCTCGAG                         GTCTTCATCTGTTGCACTCATGATTTAGCACCAGCTGAAGTGACCTCTGAG
genomic: CATGCCCTAGCACGCGCCGCGCAGCCTACGAGCGGGAGCCACACCTCGAGgtaaccacca ... atttttacagGTCTTCATCTGTTGCACTCATGATTTAGCACCAGCTGAAGTGACCTCTGAG
EST: gi|88761787|gb|CI771343.1|CI771343
EST:     CATGCCCTAGCACGCGCCGCGCAGCCTACGAGCGGGAGCCACACCTCGAG                         GTCTTCATCTGTTGCACTCATGATTTAGCACCAGCTGAAGTGACCTCTGAG
genomic: CATGCCCTAGCACGCGCCGCGCAGCCTACGAGCGGGAGCCACACCTCGAGgtaaccacca ... atttttacagGTCTTCATCTGTTGCACTCATGATTTAGCACCAGCTGAAGTGACCTCTGAG

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 1 RNA-Seqlibrary.


Block sizes: 71 (upstream exon), 73 (downstream exon)
Score: 37

GAGCGCAACAAAAGGAAAGCAGGGAAACCTCGCCGTCCTCTCTCTCCATCCATGCCCTAGCACGCGCCGCGCAGCCTACGAGCGGGAGCCACACCTCGAGgtaaccacca ... atttttacagGTCTTCATCTGTTGCACTCATGATTTAGCACCAGCTGAAGTGACCTCTGAGACTGCGCGGTGACGTAGCCTGTTGCTAGGATAAAAATCTCAGTAGTTAA




<











<


<









Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GAGCGCAACAAAAGGAAAGCAGGGAAACCTCGCCGTCCTCTCTCTCCATCCATGCCCTAGCACGCGCCGCGCAGCCTACGAGCGGGAGCCACACCTCGAGgtaaccaccaccaccatcgccaccctcctcctcctcctcctcctcttctcccctcgatcccgtccgatcaaaaccctagcaccctccgcgcggcgctggc

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -caccacc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cgccacc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cctcctc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cccctcg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cccgtcc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ccctccg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cgcggcg